/*
* Annotations count
*/
private void addAnnotationReport(GeneSetAnalysis fatiscan, String dbName) {
DecimalFormat formatter = new DecimalFormat("#######.##");
double list1Percentage =
((double) (fatiscan.getAnnotatedCounter()) / (double) fatiscan.getIdList().size()) * 100.0;
String listMessage =
fatiscan.getAnnotatedCounter()
+ " of "
+ fatiscan.getIdList().size()
+ " ("
+ formatter.format(list1Percentage)
+ "%) "
+ formatter.format(fatiscan.getMeanAnnotationsPerId())
+ " annotations/id";
annotationReport.append(dbName).append("\t").append(listMessage).append("\n");
}
private void doYourAnnotationsTest(
FeatureData rankedList, FeatureList<AnnotationItem> annotations, Method method)
throws IOException, SQLException, IllegalAccessException, ClassNotFoundException,
InstantiationException, InvalidParameterException, InvalidIndexException {
// db attributes
FunctionalDbDescriptor filterInfo =
new FunctionalDbDescriptor(
"your_annotation", "Your annotations", "your_annotations", "Your annotations");
// get term sizes
Map<String, Integer> termSizes = getYourAnnotationsTermSizes();
logger.info(filterInfo.getTitle() + "...\n");
GeneSetAnalysis gsea;
if (method == Method.Logistic) {
gsea = new LogisticScan(rankedList, annotations, order);
} else {
gsea =
new FatiScan(
rankedList,
annotations,
numberOfPartitions,
testMode,
outputFormat,
order,
duplicatesMode);
}
// run
try {
gsea.setLogger(logger);
// set term sizes
gsea.setTermSizes(termSizes);
gsea.run();
// save results
saveGeneSetAnalysisResults(gsea, filterInfo);
} catch (EmptyAnnotationException ene) {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"No annotation was found for " + filterInfo.getTitle() + " ids",
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Annotation files"));
} catch (Exception ene) {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"Unexpected error was found while running analysis for "
+ filterInfo.getTitle()
+ " ids",
filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("ERROR"),
new HashMap<String, String>(),
"All results"));
ene.printStackTrace();
}
logger.info("...end of " + filterInfo.getTitle());
}
private void saveGeneSetAnalysisResults(GeneSetAnalysis gsea, FunctionalDbDescriptor filterInfo)
throws IOException {
String fileName = filterInfo.getName() + ".txt";
String annotFileName = filterInfo.getName() + ".annot";
// save statistic results
IOUtils.write(outdir + "/" + fileName, ListUtils.toString(gsea.resultsToStringList(), "\n"));
result.addOutputItem(
new Item(
filterInfo.getName(),
fileName,
filterInfo.getTitle(),
Item.TYPE.FILE,
Arrays.asList(filterInfo.getPrefix().toUpperCase() + "_TERM"),
new HashMap<String, String>(),
"All results"));
// save significant results
int numberOfSignificantTerms;
List<GeneSetAnalysisTestResult> significant;
String formattedPValue;
for (int i = 0; i < DEFAULT_PVALUES.length; i++) {
formattedPValue = pvalueFormatter.format(DEFAULT_PVALUES[i]);
significant = gsea.getSignificant(DEFAULT_PVALUES[i]);
if (significant != null && significant.size() > 0) {
IOUtils.write(
outdir + "/significant_" + filterInfo.getName() + "_" + formattedPValue + ".txt",
gsea.significantResultsToStringList(significant, DEFAULT_PVALUES[i]));
numberOfSignificantTerms = significant.size();
} else {
numberOfSignificantTerms = 0;
}
significantCount
.get(i)
.append(filterInfo.getTitle())
.append("\t")
.append(numberOfSignificantTerms)
.append("\n");
if (numberOfSignificantTerms > 0) {
// go graph
if (filterInfo.getPrefix().equalsIgnoreCase("go")) {
try {
String limitMessage = "";
boolean outOfbounds = createGseaGoGraph(significant, DEFAULT_PVALUES[i], filterInfo);
if (outOfbounds) limitMessage = " just most 100 significant terms";
Item item =
new Item(
"go_graph_significant_" + filterInfo.getName() + "_" + formattedPValue,
"go_graph_" + filterInfo.getName() + "_" + formattedPValue + "_graphimage.png",
filterInfo.getTitle()
+ " DAG (significant terms, pvalue<"
+ formattedPValue
+ ") "
+ limitMessage,
Item.TYPE.IMAGE,
Arrays.asList("SIGNIFICANT,THUMBNAIL,GO_GRAPH_VIZ_JNLP"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
} catch (GoGraphException gge) {
Item item =
new Item(
"go_graph_significant_" + filterInfo.getName() + "_" + formattedPValue,
"Graph not found",
filterInfo.getTitle()
+ " DAG (significant terms, pvalue<"
+ formattedPValue
+ ")",
Item.TYPE.MESSAGE,
Arrays.asList("ERROR"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
}
}
// table
Item item =
new Item(
"significant_" + filterInfo.getName(),
"significant_" + filterInfo.getName() + "_" + formattedPValue + ".txt",
filterInfo.getTitle() + " significant terms (pvalue<" + formattedPValue + ")",
Item.TYPE.FILE,
Arrays.asList(
"SIGNIFICANT",
"TABLE",
gsea.getMethod().toUpperCase() + "_TABLE",
filterInfo.getPrefix().toUpperCase() + "_TERM"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
} else {
Item item =
new Item(
"significant_" + filterInfo.getName(),
"No significant terms for current pvalue " + formattedPValue,
filterInfo.getTitle() + " significant terms (pvalue<" + formattedPValue + ")",
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Significant Results." + filterInfo.getTitle());
item.setContext("pvalue==" + formattedPValue);
result.getOutputItems().add(4, item);
}
}
// annotations report
addAnnotationReport(gsea, filterInfo.getTitle());
// save annotations
if (gsea.getAnnotations() != null && gsea.getAnnotations().size() > 0) {
IOUtils.write(outdir + "/" + annotFileName, gsea.getAnnotations().toString());
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
annotFileName,
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.FILE,
Arrays.asList("ANNOTATION"),
new HashMap<String, String>(),
"Annotation files"));
} else {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"no annotations found for input ids",
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Annotation files"));
}
}
private void doTest(FeatureData rankedList, FunctionalFilter filter, Method method)
throws SQLException, IllegalAccessException, ClassNotFoundException, InstantiationException {
// db attributes
FunctionalDbDescriptor filterInfo = new FunctionalDbDescriptor(filter);
// get term sizes
// AnnotationDBManager adbm = new AnnotationDBManager(dbConnector);
// Map<String, Integer> termSizes = adbm.getAnnotationTermsSize(filterInfo.getPrefix());
logger.info(filterInfo.getTitle() + "...\n");
GeneSetAnalysis gsea;
if (method == Method.Logistic) {
gsea = new LogisticScan(rankedList, filter, species, order);
((LogisticScan) gsea).setWorkingDirectory(outdir);
} else {
gsea =
new FatiScan(
rankedList,
filter,
null,
numberOfPartitions,
testMode,
outputFormat,
order,
duplicatesMode);
}
// run
try {
gsea.setLogger(logger);
// set term sizes
// gsea.setTermSizes(termSizes);
gsea.run();
logger.print("saving results...");
// save results
saveGeneSetAnalysisResults(gsea, filterInfo);
logger.println("OK");
} catch (EmptyAnnotationException ene) {
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"No annotation was found for " + filterInfo.getTitle() + " ids",
"Annotations for " + filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("WARNING"),
new HashMap<String, String>(),
"Annotation files"));
} catch (Exception ene) {
ene.printStackTrace();
result.addOutputItem(
new Item(
"annot_" + filterInfo.getName(),
"Unexpected error was found while running analysis for "
+ filterInfo.getTitle()
+ " ids",
filterInfo.getTitle(),
Item.TYPE.MESSAGE,
Arrays.asList("ERROR"),
new HashMap<String, String>(),
"All results"));
}
logger.info("...end of " + filterInfo.getTitle());
}